The study of simian immunodeficiency virus (SIV) infection in Asian macaques has provided numerous insights into the pathogenesis of AIDS in human immunodeficiency virus type 1 (HIV-1)-infected humans. The divergence of the envelope glycoproteins of SIVmac and HIV-1, however, limit the utility of the SIVmac model for studying HIV-1 envelope glycoprotein determinants of pathogenicity, and for testing vaccine strategies directed against the HIV-1 envelope glycoproteins. In vivo passage of a chimeric simian-human immunodeficiency virus (SHIV-89.6) expressing HIV-1 tat, rev, vpu and env genes generated pathogenic virus (SHIV-89.6P) inducing rapid CD4+ lymphocyte depletion and AIDS-like illness in rhesus monkeys (J Virol 70:6922-6928, 1996). Virus generated from some proviral clones of SHIV-89.6P caused a rapid and profound decline of CD4+ lymphocytes in a high percentage of inoculated macaques. Nucleotide changes potentially responsible for increased virulence of SHIV-89.6P were limited to the env, tat or long terminal repeat sequences, with most of the observed changes in env. Nucleotide changes in env altered 12 amino acids in the gp120 and gp41 exterior domains, and a 140 bp deletion in env resulted in the substitution of the carboxyl terminus of the SIVmac gp41 glycoprotein for that of the HIV-1 gp41 glycoprotein. The availability of pathogenic proviral clones should facilitate dissection of the molecular determinant of SHIV-89.6P virulence and the evaluation of HIV-1 vaccine strategies.